Modal Codon Usage: Assessing the Typical Codon Usage of a Genome

Davis, J. J.; Olsen, G. J.

doi:10.1093/molbev/msp281

Title: Modal Codon Usage: Assessing the Typical Codon Usage of a Genome

Journal Article · 16 December 2009 · Molecular Biology and Evolution

DOI: https://doi.org/10.1093/molbev/msp281 · OSTI ID:1625393

Davis, J. J. ^[1]; Olsen, G. J. ^[2]

Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Microbiology; DOE/OSTI
Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Microbiology; Univ. of Illinois at Urbana-Champaign, IL (United States). Inst. for Genomic Biology

Most genomes are heterogeneous in codon usage, so a codon usage study should start by defining the codon usage that is typical to the genome. Although this is commonly taken to be the genomewide average, we propose that the mode—the codon usage that matches the most genes—provides a more useful approximation of the typical codon usage of a genome. We provide a method for estimating the modal codon usage, which utilizes a continuous approximation to the number of matching genes and a simplex optimization. In a survey of bacterial and archaeal genomes, as many as 20% more of the genes in a given genome match the modal codon usage than the average codon usage. We use the mode to examine the evolution of the multireplicon genomes of Agrobacterium tumefaciens C58 and Borrelia burgdorferi B31. In A. tumefaciens, the circular and linear chromosomes are characterized by a common ‘‘chromosome-like’’ codon usage, whereas both plasmids share a distinct ‘‘plasmid-like’’ codon usage. In B. burgdorferi, in addition to different codon-usage biases on the leading and lagging strands of DNA replication found by McInerney (McInerney JO. 1998. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA. 95:10698–10703), we also detect a codon-usage similarity between linear plasmid lp38 and the leading strand of the chromosome and a high similarity among the cp32 family of plasmids.

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Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: FG02-01ER63146

OSTI ID:: 1625393

Journal Information:: Molecular Biology and Evolution, Journal Name: Molecular Biology and Evolution Journal Issue: 4 Vol. 27; ISSN 0737-4038

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Evolutionary Biology
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codon adaptation index
correspondence analysis
horizontal gene transfer

Title: Modal Codon Usage: Assessing the Typical Codon Usage of a Genome

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